Posts
2021
September 22, 2021
I use pandoc for converting markdown into PDF. Using LaTeX templates, I can make nice-looking PDFs output that, in my opinion, look as good as a professional publication. But one challenge I've struggled with is how to handle supplementary citations. Here, I outline the problem and describe a lua filter I wrote to solve it.
January 12, 2021
Video conferencing is on the rise, but people are still learning how to use it. It's convenient in many ways, but also comes with some new challenges that make it harder to communicate than talking face-to-face. In this post I share some specific things I've learned about how to improve communication and reduce fatigue when using video technology.
2020
November 23, 2020
Want to switch from legacy HPC environment modules and upgrade to linux containers, so you can re-use them on multiple servers? Here's how I did it.
2019
February 26, 2019
PERSPECTIVE: The democratization of scientific publication
What's next for the revolution in scientific publishing? The scientific publishing industry is facing challenges to pillars of tradition like peer review and journal subscription. In the face of these challenges, the traditional roles of scientific publishers are deteriorating. New tools are now putting scientific publication within reach of the masses, leading to an explosion of new journals and funding models. As the material cost to publish a scientific paper approaches zero, what stops a scientist from simply self-publishing research? Here, I present my experience building a basic self-publishing system and my perspective on the changing modes of scholarly publication.
2018
2017
August 21, 2017
Many common bioinformatic tasks are embarrassingly parallel, and there are many ways to parallelize. The way you decide to parallelize will affect both performance and developer cost, and choosing the best way in practice depends on the specifics of the project. To implement parallelism in a project usually requires significant developer resources, and unfortunately, in my opinion these resources are not always well-spent. This post summarizes my experience with parallelism in bioinformatics into a few useful concepts to guide how to employ it to the greatest benefit in terms of both computational efficiency and respect for developer time.
2016
2015
2011
2009